Mite treatment and Supers

Hi there. I am a two year old bee keeper so still trying to figure out these rascals. I am in Austin Texas and the flow for the most part is over for the summer and time to really pay attention to the mite treatments.
In the Texas summer heat, the only mite treatment recommended is Apivar. I have a super on one hive that only has 2 1/3rd capped sections of honey. Not really enough to harvest so figure I will just leave it. I have heard you need to remove the supers when you treat for mites. But, does it matter if there are not significant stores of honey or is it an absolute that the super must be removed before treating? Thanks in advance for helping a newbie!! Eric